\section{NFcore Namespace Reference}
\label{namespaceNFcore}\index{NFcore@{NFcore}}


\subsection{Detailed Description}
Contains the primary classes and functions of NFsim. 

This namespace contains all the basic components needed for a typical simulation in NFsim. The main classes are defined in the \doxyref{NFcore.hh}{p.}{NFcore_8hh} header file for convenience, but the actual definitions are in the appropriately named cpp files. Additional classes in the \doxyref{NFcore}{p.}{namespaceNFcore} namespace for handling reactions, functions, modules, and other features are spread throughout the code. When developing NFsim, it is advisable to work in this namespace if you are working on core NFsim functionality. If, instead, you are merely putting in an add on or manipulating a \doxyref{System}{p.}{classNFcore_1_1System}, you should create a new namespace. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}




\subsection*{Classes}
\begin{CompactItemize}
\item 
class {\bf MoleculeList}
\begin{CompactList}\small\item\em Keeps a set of molecules neatly for a \doxyref{MoleculeType}{p.}{classNFcore_1_1MoleculeType}. \item\end{CompactList}\item 
class {\bf ComplexList}
\begin{CompactList}\small\item\em Container to organize all system complexes. \item\end{CompactList}\item 
class {\bf System}
\begin{CompactList}\small\item\em The main class that begins and runs simulations. \item\end{CompactList}\item 
class {\bf MoleculeType}
\begin{CompactList}\small\item\em Keeps track of the types of molecules that can exist. \item\end{CompactList}\item 
class {\bf Molecule}
\begin{CompactList}\small\item\em Each molecule in the system is represented by an instance of this. \item\end{CompactList}\item 
class {\bf ReactionClass}
\begin{CompactList}\small\item\em Abstract Base Class that defines the interface for all reaction rules. \item\end{CompactList}\item 
class {\bf Complex}
\begin{CompactList}\small\item\em Container to dynamically keep track of all system complexes. \item\end{CompactList}\item 
class {\bf Observable}
\begin{CompactList}\small\item\em Tracks the counts of predefined observables in the simulation. \item\end{CompactList}\item 
class {\bf MoleculesObservable}
\item 
class {\bf SpeciesObservable}
\item 
class {\bf ReactionSelector}
\item 
class {\bf DirectSelector}
\item 
class {\bf LogClassSelector}
\item 
class {\bf TemplateMolecule}
\begin{CompactList}\small\item\em Used for matching \doxyref{Molecule}{p.}{classNFcore_1_1Molecule} objects to the given pattern. \item\end{CompactList}\item 
class {\bf FuncFactory}
\begin{CompactList}\small\item\em Parses mathmatical functions that can be easily used anywhere. \item\end{CompactList}\item 
class {\bf GlobalFunction}
\begin{CompactList}\small\item\em Defines functions to be used globally in a simulation. \item\end{CompactList}\item 
class {\bf FunctionReference}
\item 
class {\bf StateCounter}
\item 
class {\bf LocalFunction}
\item 
class {\bf CompositeFunction}
\item 
class {\bf Outputter}
\item 
class {\bf DumpSystem}
\begin{CompactList}\small\item\em Class for outputting the state of the system. \item\end{CompactList}\item 
class {\bf Mapping}
\begin{CompactList}\small\item\em Keeps a pointer to a molecule and remembers a single component to act on. \item\end{CompactList}\item 
class {\bf MapGenerator}
\begin{CompactList}\small\item\em Knows how to assign mappings in a \doxyref{MappingSet}{p.}{classNFcore_1_1MappingSet} to a particular \doxyref{Molecule}{p.}{classNFcore_1_1Molecule}. \item\end{CompactList}\item 
class {\bf MappingSet}
\begin{CompactList}\small\item\em Keeps a list of mappings needed by a particular list of reactants. \item\end{CompactList}\item 
class {\bf ReactantContainer}
\begin{CompactList}\small\item\em Interface for all containers of Reactants (MappingSets) needed by ReactionClasses. \item\end{CompactList}\item 
class {\bf ReactantList}
\begin{CompactList}\small\item\em Maintains a list of MappingSets needed by \doxyref{ReactionClass}{p.}{classNFcore_1_1ReactionClass}. \item\end{CompactList}\item 
class {\bf ReactantTree}
\begin{CompactList}\small\item\em Maintains a tree of MappingSets needed by Distribution of Rates Reactions. \item\end{CompactList}\item 
class {\bf BasicRxnClass}
\item 
class {\bf PopulationRxnClass}
\item 
class {\bf FunctionalRxnClass}
\item 
class {\bf MMRxnClass}
\item 
class {\bf DORRxnClass}
\item 
class {\bf MoleculeCreator}
\item 
class {\bf SpeciesCreator}
\item 
class {\bf TransformationFactory}
\item 
class {\bf Transformation}
\item 
class {\bf LocalFunctionReference}
\item 
class {\bf EmptyTransform}
\item 
class {\bf StateChangeTransform}
\item 
class {\bf BindingTransform}
\item 
class {\bf BindingSeparateComplexTransform}
\item 
class {\bf UnbindingTransform}
\item 
class {\bf AddSpeciesTransform}
\item 
class {\bf AddMoleculeTransform}
\item 
class {\bf RemoveMoleculeTransform}
\item 
class {\bf DecrementPopulationTransform}
\item 
class {\bf IncrementStateTransform}
\item 
class {\bf DecrementStateTransform}
\item 
class {\bf TransformationSet}
\begin{CompactList}\small\item\em Maintains a set of \doxyref{Transformation}{p.}{classNFcore_1_1Transformation} objects for a \doxyref{ReactionClass}{p.}{classNFcore_1_1ReactionClass}. \item\end{CompactList}\end{CompactItemize}
\subsection*{Functions}
\begin{CompactItemize}
\item 
void {\bf test} ()
\item 
void {\bf test\_\-tree} ()
\item 
void {\bf test\_\-simple} ()
\end{CompactItemize}


\subsection{Function Documentation}
\index{NFcore@{NFcore}!test@{test}}
\index{test@{test}!NFcore@{NFcore}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void NFcore::test ()}\label{namespaceNFcore_6b8b82ec0d793146a5a6aedbd5338e25}


Function used for initial testing of the entire \char`\"{}mapping\char`\"{} construct including MappingSets, TransformationSets, ReactantLists, etc. \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFcore@{NFcore}!test\_\-simple@{test\_\-simple}}
\index{test\_\-simple@{test\_\-simple}!NFcore@{NFcore}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void NFcore::test\_\-simple ()}\label{namespaceNFcore_aa63919c98caf55b6b95a61b4d565621}


Some very simple initial testing and debugging of ReactantLists and the rest of the mapping functions unter NFreactions \begin{Desc}
\item[Author:]Michael Sneddon \end{Desc}
\index{NFcore@{NFcore}!test\_\-tree@{test\_\-tree}}
\index{test\_\-tree@{test\_\-tree}!NFcore@{NFcore}}
\subsubsection{\setlength{\rightskip}{0pt plus 5cm}void NFcore::test\_\-tree ()}\label{namespaceNFcore_638f68bc48f243c3998ad6aacbbcdd1d}


